Figure 3. Association of metabolic proteins in crowded environments.
(A) Intermolecular distance changes between initial and final time (ΔdAB) for pairs of glycolytic enzymes, other regular proteins, RNAs, and ribosomes/GroEL (huge). (B) Solvation free energies ΔGsol normalized by the solvent-accessible surface area (SASA) for equilibrated copies of macromolecules in MGm1 using GBMV (Lee et al., 2003) in CHARMM (Brooks et al., 2009). See also supplementary Figure 1 showing the influence of large macromolecules on the association of small proteins based on simple Lennard-Jones mixtures.
Figure 3—figure supplement 1. Influence of large macromolecules on the association of small proteins.
(A−D) Two-component mixtures of small Lennard-Jones particles ‘A’ (2 Å, white) in the presence of same size particles ‘B’ (LJ_AB) or in the presence of larger particles ‘C’ (3.509 Å, LJ_AC) or ‘D’ (5.570 Å, LJ_AD) occupying the same volume (3400 Å3) in a (18.666 Å)3 cubic box. In an additional simulation, LJ_AD_rep, the ‘D’ particle had a unit charge to create repulsion. (E) Pairwise density distribution function ρ(r) for ‘A’ particles in LJ_AB (blue), in LJ_AC (green), LJ_AD (red) and LJ_AD_rep (dashed red). (F) Cumulative numbers of particles within spherical shells around ‘A’ particles show an extra particle in LJ_AD and LJ_AD_rep beyond r = 4 Å but with the difference disappearing in LJ_AD_rep at 6 Å.